Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011682.1 Corchorus olitorius cultivar O-4 contig11715, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 1994
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38


Found at i:285 original size:154 final size:154

Alignment explanation


    Indices: 1--1347  Score: 2018
    Period size: 154  Copynumber: 8.7  Consensus size: 154

                    *   *      *     *      *                            **  
          1 AACACTTGCTATTTTGGGCTTATCGAGGCCCAATAGTGACGTTTTGAATCGTCTTCGATTTCTCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                                         *                   
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCGTTTTGGTAAGATTAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

              *            *  *      
        131 CTTTGTAAGTTTTTATCTAATTTGG
        131 CTGTG-AAGTTTTTAGCTCATTTGG

                    *             *         *    **      *                *  
        156 AACACTTGATATATTGGGCCTAACGGGGCCCAATAGTTCCG-TTTAAATCGTCTTCGATTTGACA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                   *                              *   *  *   
        220 ACCCTCAATG-TTTTCCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTTAGACTAATCC
         66 ACCCTCAATGCTTTT-CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCC

               *                     
        284 ACTTTGAAGTTTTTAGCTCATTTGG
        130 ACTGTGAAGTTTTTAGCTCATTTGG

                    *   *            *      *                            **  
        309 AACACTTGCTATTTTGGGCCTATCGAGGCCCAATAGTGACGTTTTGAATCGTCTTCGATTTCTCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                 *                               * *         
        374 ACCCTCAATGCTTTTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGTGATATTAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

              *           *         
        439 CTTTGAAGTTTTTATCTCATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                   *                       *      **                       * 
        463 AACACTTTTTATATTGGGCCTAAT-GGGGCCTATTAGTTCCGTTTTGAATCGTCTTCGATTTGAC
          1 AACACTTGTTATATTGGGCCT-ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC

                           *       *                                         
        527 AACCCTCAATGCTTTCCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCC
         65 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCC

                                     
        592 ACTGTGAAGTTTTTAGCTCATTTGG
        130 ACTGTGAAGTTTTTAGCTCATTTGG

                        *     *      *                                       
        617 AACACTTGTTATTTTGGGTCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                                                             
        682 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

                             *      
        747 CTGTGAAGTTTTTAGCTAATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                    *                       *      *                         
        771 AACACTTGATATATTGGGCCTATCGGGGCCCACTAGTGATGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

             *                      *                         *  *          *
        836 AACCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCG
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

                                    
        901 CTGTGAAGTTTTTAGCTCATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                                  *              **                          
        925 AACACTTGTTATATTGGGCCTAACGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

             *                                                   *           
        990 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

                                    
       1055 CTGTGAAGTTTTTAGCTCATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                        *            *   *                                *  
       1079 AACACTTGTTATTTTGGGCCTATCGAGGCTCATTAGTGACGTTTTGAATCGTCTTCGATTTGTCA
          1 AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA

                                  *                                          
       1144 ACCCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA

              *           *         
       1209 CTTTGAAGTTTTTATCTCATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                                                  **                         
       1233 AACACTTGTTATATTGGGCCTAAT-GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
          1 AACACTTGTTATATTGGGCCT-ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC

              *                                                
       1297 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
         65 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT

       1348 TGATGCGCCA


Statistics
Matches: 1084,  Mismatches: 102, Indels: 13
        0.90            0.09        0.01

Matches are distributed among these distances:
 153   58  0.05
 154  984  0.91
 155   42  0.04

ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41


Consensus pattern (154 bp):   
AACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGG

Found at i:1483 original size:21 final size:21

Alignment explanation


    Indices: 1457--1498  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1447 TAAGGAAGAA

                                 
       1457 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
       1478 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

       1499 TCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.